Ana Galhoz
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: RELEASE_3_16 |
| git_last_commit: cd4b58e |
| git_last_commit_date: 2022-11-01 11:24:35 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:32 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the wppi package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wppi.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2165/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.6.0 (landing page) Ana Galhoz
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: wppi |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.6.0.tar.gz |
| StartedAt: 2023-04-10 23:20:41 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:23:54 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 192.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/wppi.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘wppi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2023-04-10 23:21:15] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-04-10 23:21:15] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-04-10 23:21:15] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-04-10 23:21:15] [TRACE] [OmnipathR] Contains 1 files.
[2023-04-10 23:21:15] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-04-10 23:21:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-04-10 23:21:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-10 23:21:15] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
wppi 27.377 0.605 28.070
score_candidate_genes_from_PPI 14.252 0.342 14.621
prioritization_genes 13.812 0.319 14.156
random_walk 13.706 0.241 13.980
weighted_adj 10.380 0.236 10.653
count_genes 7.231 0.891 7.258
wppi_data 5.647 0.115 5.778
filter_annot_with_network 5.582 0.156 5.760
common_neighbors 5.182 0.260 11.093
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.16-bioc/meat/wppi.Rcheck/00check.log’
for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2023-04-10 15:19:01] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:19:01] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-10 15:19:01] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:19:01] [TRACE] [OmnipathR] Contains 1 files. [2023-04-10 15:19:01] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-10 15:19:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:19:01] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-10 15:19:01] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2023-04-10 15:19:05] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:19:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-10 15:19:05] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:19:05] [TRACE] [OmnipathR] Contains 1 files. [2023-04-10 15:19:05] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-10 15:19:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:19:06] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-10 15:19:06] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-04-10 15:19:09] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:19:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-10 15:19:09] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:19:09] [TRACE] [OmnipathR] Contains 1 files. [2023-04-10 15:19:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-10 15:19:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-04-10 15:19:09] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-10 15:19:09] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi)
wppi.Rcheck/wppi-Ex.timings
| name | user | system | elapsed | |
| common_neighbors | 5.182 | 0.260 | 11.093 | |
| count_genes | 7.231 | 0.891 | 7.258 | |
| filter_annot_with_network | 5.582 | 0.156 | 5.760 | |
| functional_annot | 1.086 | 0.163 | 2.067 | |
| graph_from_op | 2.940 | 0.037 | 2.980 | |
| in_omnipath | 2.981 | 0.033 | 3.020 | |
| prioritization_genes | 13.812 | 0.319 | 14.156 | |
| process_annot | 0.460 | 0.006 | 0.468 | |
| random_walk | 13.706 | 0.241 | 13.980 | |
| score_candidate_genes_from_PPI | 14.252 | 0.342 | 14.621 | |
| subgraph_op | 2.865 | 0.025 | 2.894 | |
| weighted_adj | 10.380 | 0.236 | 10.653 | |
| wppi | 27.377 | 0.605 | 28.070 | |
| wppi_data | 5.647 | 0.115 | 5.778 | |
| wppi_go_data | 2.452 | 0.113 | 2.577 | |
| wppi_hpo_data | 0.309 | 0.004 | 0.314 | |
| wppi_omnipath_data | 2.525 | 0.019 | 2.547 | |